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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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Error: Could not find tools necessary to compile a package #233

Open lexie-lee opened 1 week ago

lexie-lee commented 1 week ago

Hi,

I met a error when I try to install cellchat.

I installed the NMF, umap according to your tutorial.

but when I try to install cellchat using "devtools::install_github("jinworks/CellChat")"

I met the error:

Error: Failed to install 'CellChat' from GitHub:
  Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

when I callpkgbuild::check_build_tools(debug = TRUE)

it says:

Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
/usr/local/clang4/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c foo.c -o foo.o
/bin/sh: /usr/local/clang4/bin/clang: No such file or directory
make: *** [foo.o] Error 127
Error: Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

I checked the clang version is 9.0.0. and I also configured my bash file, it still doesn't work.

is there any suggestions? can you help me solve this?

Thanks.

lexie-lee commented 1 week ago

and the sessioninfo is:

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 14.5

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dbplyr_2.3.2

loaded via a namespace (and not attached):
  [1] fgsea_1.24.0           colorspace_2.1-0       ggtree_3.6.2          
  [4] gson_0.1.0             ellipsis_0.3.2         qvalue_2.30.0         
  [7] XVector_0.38.0         fs_1.6.1               aplot_0.1.10          
 [10] rstudioapi_0.14        farver_2.1.1           remotes_2.4.2         
 [13] graphlayouts_0.8.4     ggrepel_0.9.3          bit64_4.0.5           
 [16] AnnotationDbi_1.60.2   fansi_1.0.4            scatterpie_0.1.8      
 [19] codetools_0.2-19       splines_4.2.2          cachem_1.0.7          
 [22] GOSemSim_2.24.0        pkgload_1.3.2          polyclip_1.10-4       
 [25] jsonlite_1.8.4         GO.db_3.16.0           png_0.1-8             
 [28] ggforce_0.4.1          shiny_1.7.4            compiler_4.2.2        
 [31] httr_1.4.5             Matrix_1.5-4           fastmap_1.1.1         
 [34] lazyeval_0.2.2         cli_3.6.1              later_1.3.0           
 [37] tweenr_2.0.2           prettyunits_1.1.1      htmltools_0.5.5       
 [40] tools_4.2.2            igraph_1.4.1           gtable_0.3.3          
 [43] glue_1.6.2             GenomeInfoDbData_1.2.9 reshape2_1.4.4        
 [46] dplyr_1.1.1            fastmatch_1.1-3        Rcpp_1.0.10           
 [49] enrichplot_1.18.4      Biobase_2.58.0         vctrs_0.6.1           
 [52] Biostrings_2.66.0      ape_5.7-1              nlme_3.1-162          
 [55] ggraph_2.1.0           stringr_1.5.0          ps_1.7.4              
 [58] sceasy_0.0.7           mime_0.12              miniUI_0.1.1.1        
 [61] lifecycle_1.0.3        clusterProfiler_4.6.2  devtools_2.4.5        
 [64] DOSE_3.24.2            zlibbioc_1.44.0        MASS_7.3-58.3         
 [67] scales_1.2.1           tidygraph_1.2.3        promises_1.2.0.1      
 [70] parallel_4.2.2         RColorBrewer_1.1-3     curl_5.0.0            
 [73] reticulate_1.28        memoise_2.0.1          gridExtra_2.3         
 [76] ggplot2_3.4.2          downloader_0.4         ggfun_0.0.9           
 [79] HDO.db_0.99.1          yulab.utils_0.0.6      stringi_1.7.12        
 [82] RSQLite_2.3.1          S4Vectors_0.36.2       tidytree_0.4.2        
 [85] BiocGenerics_0.44.0    pkgbuild_1.4.0         BiocParallel_1.32.6   
 [88] GenomeInfoDb_1.34.9    rlang_1.1.0            pkgconfig_2.0.3       
 [91] bitops_1.0-7           lattice_0.21-8         purrr_1.0.1           
 [94] htmlwidgets_1.6.2      treeio_1.22.0          patchwork_1.1.2       
 [97] processx_3.8.0         cowplot_1.1.1          shadowtext_0.1.2      
[100] bit_4.0.5              tidyselect_1.2.0       plyr_1.8.8            
[103] magrittr_2.0.3         R6_2.5.1               profvis_0.3.8         
[106] IRanges_2.32.0         generics_0.1.3         DBI_1.1.3             
[109] pillar_1.9.0           withr_2.5.0            KEGGREST_1.38.0       
[112] RCurl_1.98-1.12        tibble_3.2.1           crayon_1.5.2          
[115] utf8_1.2.3             urlchecker_1.0.1       usethis_2.1.6         
[118] viridis_0.6.2          grid_4.2.2             data.table_1.14.8     
[121] callr_3.7.3            blob_1.2.4             digest_0.6.31         
[124] xtable_1.8-4           tidyr_1.3.0            httpuv_1.6.9          
[127] gridGraphics_0.5-1     stats4_4.2.2           munsell_0.5.0         
[130] viridisLite_0.4.1      ggplotify_0.1.0        sessioninfo_1.2.2